A transcriptionally active maize MuDR-like transposable element in rice and its relatives

Two Mu-like transposable elements were cloned from a rice genomic library using a partial cDNA clone that exhibits high homology to the mudrA gene of the maize element MuDR. Database searches led to the identification of six other sequences that carried highly homologous terminal inverted repeats (TIRs). All the rice elements possessed approximately 200-bp TIRs, and four were flanked by 9-bp target-site duplications (TSDs). The longer of the two cloned elements, OsMu4-2, could potentially encode a protein colinear with a MURA-like transposase, but it had stop codons in the coding region indicating that it is a pseudogene. All the other elements had large internal deletions. Direct dinucleotide repeats were found in two elements at positions flanking the deleted regions, suggesting that the deletions arose via the interrupted-gap-repair mechanism. Sequences related to empty sites of insertion were found in OsMu4-2 and one of the elements identified in the databases. These results provide evidence that the rice OsMu element was active and transposed in the past. Analysis of OsMu4-2 cDNAs revealed two types of transcripts produced by alternative splicing. Genomic Southern analysis suggested that OsMu4-2 was conserved in rice species with the A genome, but a deleted version was unique to japonica subspecies. Some wild rice species harbored paralogous copies of the OsMu element.